EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.Author summary: Poultry meat is important for improving nutrition in developing countries. However, the rapid growth of poultry production raises concerns about the risks of diseases that can be passed from animals to humans and cause outbreaks. To understand and manage these risks, we developed EPINEST, an agent-based modelling framework that allows investigating how diseases can spread within the networks of poultry farms, markets and their associated transportation systems. EPINEST can be adjusted to match the way in which poultry are raised and traded in specific countries. It considers different traits of pathogens, how they are transmitted, and how different strains or pathogen types can interact. While EPINEST was primarily developed to simulate the transmission of zoonotic pathogens (namely avian influenza, Campylobacter, Salmonella and other bacteria carrying resistance genes) in poultry populations in South and Southeast Asia, this modelling framework can also be useful for studying the transmission of other pathogens in other livestock species. EPINEST will help understand how poultry farming and trading shape pathogen spread, maintenance and evolution, and support decision-making to make poultry production safer and more sustainable.